A Zero-Knowledge Based Introduction to...
Transcript of A Zero-Knowledge Based Introduction to...
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A Zero-Knowledge Based Introduction to Biology�
Sandeep Chinchali, Jim Notwell�26 September 2014�
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Q: What is your genome?
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Q: What is your genome?
A: The sum of your hereditary information.
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Human Genome • 3 billion base pairs: A,T,G,C • Full DNA sequence in virtually all cells
• DNA is the blueprint for life:
• Cookbook with many “recipes” for proteins - genes
• Proteins do most of the work in biology
• Yet, only ~2% of the genome is protein-coding genes!
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What does the rest of the genome do? • 3 billion base pairs – 2% coding, 5-10% regulatory • Organism’s complexity NOT correlated with number of genes!
• Human (20-25k genes) vs. Rice (51k genes) • 1 million Regulatory elements (switches) enable:
• Precise control for turning genes on/off • Diverse cell types (lung, heart, skin)
• Analogy: Making specific recipes (genes) from a large cookbook (genome) at a given time
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Quick Recap
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DNA: “Blueprints” for a cell�
• Genetic information encoded in long strings
• Deoxyribonucleic acid (DNA) comes in four bases: adenine (A), thymine (T), guanine (G) , and cytosine (C)
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From DNA to Organism�
You are composed of ~ 10 trillion cells
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From DNA to Organism Cell�
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From DNA to Organism Cell Protein�
Proteins do most of the work in biology
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Q: How does one genome encode a variety of cell types in a complex organism?
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Regulatory Elements • ~ 20-25k genes
• Expression Modulated by Regulatory elements • Enhancer, Promoters, Silencers
• CS analogy: • Genes are like variable assignments (a = 7) • Regulatory elements are control flow, complex logic
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Controlling Gene Expression • Transcription factors (TFs):
• Proteins that recognize sequence motifs in enhancers, promoters
• Combinatorial switches that turn genes on/off
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How does the genome influence human disease?
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Bejerano Lab
Disease Implications
SHH
MUTATIONS
• Brain
• Limb
• Other
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Bejerano Lab
Limb Enhancer 1Mb away from Gene
SHH limb
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Bejerano Lab
SHH
Enhancer Deletion
limb
DELETE
• Limb
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Bejerano Lab
SHH
Enhancer 1bp Substitution
limb
MUTATIONS
• Limb
Lettice et al. HMG 2003 12: 1725-35
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Genome Wide Assocation Study (GWAS): 80% of GWAS SNPs are noncoding (hard to interpret)
Active area of research
Bejerano Lab
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How exactly do genes code for proteins?
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Central Dogma of Biology�
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DNA: “Blueprints” for a cell�
• Genetic information encoded in long strings
• Deoxyribonucleic acid comes in four bases: adenine, thymine, guanine, and cytosine
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Nucleobase Complementary Pairing �
Adenine (A) �
Cytosine (C) �
Guanine (G) �
Thymine (T) �
pyrimidines �
purines �
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DNA Double Helix �
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DNA Packaging�
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Q: What is your genome?
A:The sum of your hereditary information.
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Q: What is your genome?
A:The sum of your hereditary information. Humans bundle two copies of the genome into 46 chromosomes in every cell
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Central Dogma of Biology�
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DNA vs RNA�
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RNA Nucleobases �
Adenine (A) �
Cytosine (C) �
Guanine (G) �
Uracil (U) �
pyrimidines �
purines �
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Gene Transcription�
3’�5’�
5’�3’�
G A T T A C A . . .�
C T A A T G T . . .�
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Gene Transcription�
3’�5’�
5’�3’�
G A T T A C A . . .�
C T A A T G T . . .�
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Gene Transcription�
3’�5’�
5’�3’�
G A T T A C A . . .�
C T A A T G T . . .�
Strands are separated (DNA helicase)
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Gene Transcription�
3’�5’�
5’�3’�
G A T T A C
A . . .
C T A A T G T . . .
G A U U A C A
An RNA copy of the 5’→3’ sequence is created from the 3’→5’ template
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Gene Transcription�
3’�5’�
5’�3’�
G A U U A C A . . . �
G A T T A C A . . .�
C T A A T G T . . .�
pre-mRNA � 5’� 3’�
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RNA Processing �
5’ cap� poly(A) tail�
intron�exon�
mRNA �
5’ UTR� 3’ UTR�
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Gene Structure �
5’� 3’�
promoter �
5’ UTR� exons � 3’ UTR�
introns �
coding �
non-coding�
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Central Dogma of Biology�
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From RNA to Protein�• Proteins are long strings of amino acids joined by peptide bonds
• Translation from RNA sequence to amino acid sequence performed by ribosomes
• 20 amino acids → 3 RNA letters required to specify a single amino acid
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Amino Acid�Alanine
Arginine
Asparagine
Aspartate
Cysteine
Glutamate
Glutamine
Glycine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Proline
Serine
Threonine
Tryptophan
Tyrosine
Valine
C
O
N
H
C
H
H OH
R
There are 20 standard amino acids
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Translation�
The ribosome (a complex of protein and RNA) synthesizes a protein by reading the mRNA in triplets (codons). Each codon is translated to an amino acid.
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Translation�
G GGG Gly GAG Glu GCG Ala GUG Val
A GGA Gly GAA Glutamic acid (Glu) GCA Ala GUA Val
C GGC Gly GAC Asp GCC Ala GUC Val
U GGU Glycine (Gly) GAU Aspar4c acid (Asp) GCU Alanine (Ala) GUU Valine (Val)
G
G AGG Arg AAG Lys ACG Thr AUG Methionine (Met) or START
A AGA Arginine (Arg) AAA Lysine (Lys) ACA Thr AUA Ile
C AGC Ser AAC Asn ACC Thr AUC Ile
U AGU Serine (Ser) AAU Asparagine (Asn) ACU Threonine (Thr) AUU Isoleucine (Ile)
A
G CGG Arg CAG Gln CCG Pro CUG Leu
A CGA Arg CAA Glutamine (Gln) CCA Pro CUA Leu
C CGC Arg CAC His CCC Pro CUC Leu
U CGU Arginine (Arg) CAU His4dine (His) CCU Proline (Pro) CUU Leucine (Leu)
C
G UGG Tryptophan (Trp) UAG STOP UCG Ser UUG Leu
A UGA STOP UAA STOP UCA Ser UUA Leucine (Leu)
C UGC Cys UAC Tyr UCC Ser UUC Phe
U UGU Cysteine (Cys) UAU Tyrosine (Tyr) UCU Serine (Ser) UUU Phenylalanine (Phe)
U
G A C U
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Single Nucleotide Changes �
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Single Nucleotide Changes �
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Translation�
5’ . . . A U U A U G G C C U G G A C U U G A . . . 3’�
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Translation�
5’ . . . A U U A U G G C C U G G A C U U G A . . . 3’�
UTR� Met �
Start Codon�
Ala� Trp� Thr �
Stop Codon�
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Translation�
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Central Dogma of Biology�
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Different Cell Types�
Subsets of the DNA sequence determine the identity and function of different cells
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Gene Expression Regulation�• When should each gene be expressed?
• Why? Every cell has same DNA but each cell expresses different proteins.
• Signal transduction: One signal converted to another: cascade has “master regulators” turning on many proteins, which in turn each turn on many proteins
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Central Dogma of Biology�
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Transcription Regulation�• Transcription factors link to binding sites
• Complex of transcription factors forms
• Complex assists or inhibits formation of the RNA polymerase machinery
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Transcription Factor Binding Sites �• Short, degenerate DNA sequences recognized by particular transcription factors
• For complex organisms, cooperative binding of multiple transcription factors required to initiate transcription
Binding Sequence Logo �
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Transcription Regulation�
Transcription Factor A �
TF A �Binding Site �
Gene B�
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Q: What if the transcription/translation machinery makes mistakes?
Q:What is the effect in coding regions?
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Evolution = Mutation + Selection
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Structural Abnormalities �
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Single Nucleotide Changes �
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Single Nucleotide Changes �
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Evolution = Mutation + Selection
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Selection�time �
Harmful mutation� Beneficial mutation�
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Evolution = Mutation + Selection
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Summary�
Evolution = Mutation + Selection
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Summary�• All hereditary information encoded in double-stranded DNA
• Each cell in an organism has same DNA
• DNA → RNA → protein
• Proteins have many diverse roles in cell
• Gene regulation diversifies protein products within different cells
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Further Reading �• See website: cs173.stanford.edu
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Extra Slides
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Gene Regulatory Region�